High-performance GWAS implementation based on CUDA/cuBLAS. This is the code from my diploma (eq. masters) thesis. (Sorry AMD, no more time :-()
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README.md

README.md

cuGWAS

High-performance GWAS implementation based on CUDA/cuBLAS. This is the code from my diploma (eq. masters) thesis. (Sorry AMD, no more time :-()

THIS REPOSITORY IS OBSOLETE

I am currently working on integrating this work into OmicABEL so that it is easily useable for biologists. In the meantime, I uploaded my prototype here, you might have a look at it but beware that it is prototype-level code, so it might lead to your computer being eaten by a dinosaur.

The integration into OmicABEL takes place in another repository: cuOmicABEL and will hopefully be merged back into OmicABEL. Go over to that repository, please.

Installation

TODO

Usage

TODO

Terminology

The names of the variables used in my paper slightly differ from those used both in my code and in the ProbABEL paper which describes the origin of the mathematics. This is because I want the code to be closer to the ProbABEL paper, so it is more straightforward to interested users. The correspondences are the following:

  • In general, x suffixes correspond to l in the paper while g suffixes correspond to r in the paper. Thus Xx corresponds to Xl.
  • R, Rb and similar correspond to y in the paper.
  • V corresponds to M in the paper.
  • B, beta and similar correspond to r in the paper.